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commit 3c048c3ef64ddd5040f3e65c1cf2203d32035bc4 Author: Andreas Tille <[email protected]> Date: Fri Sep 19 22:34:53 2014 +0200 Patch to run gtest properly --- debian/patches/gtest.patch | 177 +++++++++++++++++++++++++++++++++++++++++++-- 1 file changed, 170 insertions(+), 7 deletions(-) diff --git a/debian/patches/gtest.patch b/debian/patches/gtest.patch index 4a09c1e..1bf6580 100644 --- a/debian/patches/gtest.patch +++ b/debian/patches/gtest.patch @@ -1,16 +1,179 @@ Author: Anthony Raymond <[email protected]> -Last-Updated: Tue, 16 Sep 2014 14:13:33 -0700 +Last-Updated: Wed, 17 Sep 2014 12:17:23 -0700 Description: Make sure gtest works properly I had to follow the instructions on this post to build libgtest.a and libgtest_main.a: http://askubuntu.com/questions/145887/why-no-library-files-installed-for-google-test ---- abyss.orig/configure.ac -+++ abyss/configure.ac -@@ -195,6 +195,7 @@ +--- a/Unittest/Makefile.am ++++ b/Unittest/Makefile.am +@@ -1,58 +1,72 @@ ++check_LIBRARIES = libgtest.a libgtest_main.a ++ ++gtest-all.cc: ++ cp $(GTEST)/src/gtest-all.cc . ++ ++gtest_main.cc: ++ cp $(GTEST)/src/gtest_main.cc . ++ ++libgtest_a_CPPFLAGS = -I$(top_srcdir) -I$(GTEST) ++libgtest_a_SOURCES = gtest-all.cc ++ ++libgtest_main_a_CPPFLAGS = -I$(top_srcdir) -I$(GTEST) ++libgtest_main_a_SOURCES = gtest_main.cc gtest-all.cc ++ + UNIT_TESTS = common_stringutil + check_PROGRAMS = common_stringutil + common_stringutil_SOURCES = Common/StringUtilTest.cpp + common_stringutil_CPPFLAGS = -I$(top_srcdir) +-common_stringutil_LDADD = $(GTEST_LIBS) ++common_stringutil_LDADD = libgtest_main.a $(GTEST_LIBS) + + UNIT_TESTS += common_histogram + check_PROGRAMS += common_histogram + common_histogram_SOURCES = Common/HistogramTest.cpp + common_histogram_CPPFLAGS = -I$(top_srcdir) +-common_histogram_LDADD = $(GTEST_LIBS) ++common_histogram_LDADD = libgtest_main.a $(GTEST_LIBS) + + UNIT_TESTS += common_bitutil + check_PROGRAMS += common_bitutil + common_bitutil_SOURCES = Common/BitUtilTest.cpp + common_bitutil_CPPFLAGS = -I$(top_srcdir) +-common_bitutil_LDADD = $(GTEST_LIBS) ++common_bitutil_LDADD = libgtest_main.a $(GTEST_LIBS) + + UNIT_TESTS += common_kmer + check_PROGRAMS += common_kmer + common_kmer_SOURCES = Common/KmerTest.cpp + common_kmer_CPPFLAGS = -I$(top_srcdir) +-common_kmer_LDADD = $(top_builddir)/Common/libcommon.a $(GTEST_LIBS) ++common_kmer_LDADD = $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS) + + UNIT_TESTS += common_sequence + check_PROGRAMS += common_sequence + common_sequence_SOURCES = Common/Sequence.cc + common_sequence_CPPFLAGS = -I$(top_srcdir) +-common_sequence_LDADD = $(top_builddir)/Common/libcommon.a $(GTEST_LIBS) ++common_sequence_LDADD = $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS) + + UNIT_TESTS += common_KmerIterator + check_PROGRAMS += common_KmerIterator + common_KmerIterator_SOURCES = Common/KmerIteratorTest.cpp + common_KmerIterator_CPPFLAGS = -I$(top_srcdir) +-common_KmerIterator_LDADD = $(top_builddir)/Common/libcommon.a $(GTEST_LIBS) ++common_KmerIterator_LDADD = $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS) + + UNIT_TESTS += common_sam + check_PROGRAMS += common_sam + common_sam_SOURCES = Common/SAM.cc + common_sam_CPPFLAGS = -I$(top_srcdir) +-common_sam_LDADD = $(top_builddir)/Common/libcommon.a $(GTEST_LIBS) ++common_sam_LDADD = $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS) + + UNIT_TESTS += BloomFilter + check_PROGRAMS += BloomFilter + BloomFilter_SOURCES = Konnector/BloomFilter.cc + BloomFilter_CPPFLAGS = -I$(top_srcdir) -I$(top_srcdir)/Common + BloomFilter_CXXFLAGS = $(AM_CXXFLAGS) $(OPENMP_CXXFLAGS) +-BloomFilter_LDADD = $(top_builddir)/Common/libcommon.a $(GTEST_LIBS) ++BloomFilter_LDADD = $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS) + + UNIT_TESTS += Konnector_DBGBloom + check_PROGRAMS += Konnector_DBGBloom + Konnector_DBGBloom_SOURCES = Konnector/DBGBloomTest.cpp + Konnector_DBGBloom_CPPFLAGS = -I$(top_srcdir) -I$(top_srcdir)/Common + Konnector_DBGBloom_CXXFLAGS = $(AM_CXXFLAGS) $(OPENMP_CXXFLAGS) +-Konnector_DBGBloom_LDADD = $(top_builddir)/Common/libcommon.a $(GTEST_LIBS) ++Konnector_DBGBloom_LDADD = $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS) + + UNIT_TESTS += Konnector_DBGBloomAlgorithms + check_PROGRAMS += Konnector_DBGBloomAlgorithms +@@ -61,38 +75,38 @@ Konnector_DBGBloomAlgorithms_CPPFLAGS = + Konnector_DBGBloomAlgorithms_CXXFLAGS = $(AM_CXXFLAGS) $(OPENMP_CXXFLAGS) + Konnector_DBGBloomAlgorithms_LDADD = \ + $(top_builddir)/Common/libcommon.a \ +- $(GTEST_LIBS) ++ libgtest_main.a $(GTEST_LIBS) + + UNIT_TESTS += graph_ConstrainedBFSVisitor + check_PROGRAMS += graph_ConstrainedBFSVisitor + graph_ConstrainedBFSVisitor_SOURCES = Graph/ConstrainedBFSVisitorTest.cpp + graph_ConstrainedBFSVisitor_CPPFLAGS = -I$(top_srcdir) -I$(top_srcdir)/Common +-graph_ConstrainedBFSVisitor_LDADD = $(top_builddir)/Common/libcommon.a $(GTEST_LIBS) ++graph_ConstrainedBFSVisitor_LDADD = $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS) + + UNIT_TESTS += graph_BidirectionalBFS + check_PROGRAMS += graph_BidirectionalBFS + graph_BidirectionalBFS_SOURCES = Graph/BidirectionalBFSTest.cpp + graph_BidirectionalBFS_CPPFLAGS = -I$(top_srcdir) -I$(top_srcdir)/Common +-graph_BidirectionalBFS_LDADD = $(top_builddir)/Common/libcommon.a $(GTEST_LIBS) ++graph_BidirectionalBFS_LDADD = $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS) + + UNIT_TESTS += graph_AllPathsSearch + check_PROGRAMS += graph_AllPathsSearch + graph_AllPathsSearch_SOURCES = Graph/AllPathsSearchTest.cpp + graph_AllPathsSearch_CPPFLAGS = -I$(top_srcdir) -I$(top_srcdir)/Common +-graph_AllPathsSearch_LDADD = $(top_builddir)/Common/libcommon.a $(GTEST_LIBS) ++graph_AllPathsSearch_LDADD = $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS) + + UNIT_TESTS += graph_HashGraph + check_PROGRAMS += graph_HashGraph + graph_HashGraph_SOURCES = Graph/HashGraphTest.cpp + graph_HashGraph_CPPFLAGS = -I$(top_srcdir) -I$(top_srcdir)/Common +-graph_HashGraph_LDADD = $(top_builddir)/Common/libcommon.a $(GTEST_LIBS) ++graph_HashGraph_LDADD = $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS) + + UNIT_TESTS += graph_ConstrainedBidiBFSVisitor + check_PROGRAMS += graph_ConstrainedBidiBFSVisitor + graph_ConstrainedBidiBFSVisitor_SOURCES = \ + Graph/ConstrainedBidiBFSVisitorTest.cpp + graph_ConstrainedBidiBFSVisitor_CPPFLAGS = -I$(top_srcdir) -I$(top_srcdir)/Common +-graph_ConstrainedBidiBFSVisitor_LDADD = $(top_builddir)/Common/libcommon.a $(GTEST_LIBS) ++graph_ConstrainedBidiBFSVisitor_LDADD = $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS) + + UNIT_TESTS += Konnector_konnector + check_PROGRAMS += Konnector_konnector +@@ -102,7 +116,7 @@ Konnector_konnector_CPPFLAGS = -I$(top_s + Konnector_konnector_CXXFLAGS = $(AM_CXXFLAGS) $(OPENMP_CXXFLAGS) + Konnector_konnector_LDADD = \ + $(top_builddir)/Align/libalign.a \ +- $(top_builddir)/Common/libcommon.a $(GTEST_LIBS) ++ $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS) + + ##Tests for log kmer counting / Counting bloom filter + +--- a/configure.ac ++++ b/configure.ac +@@ -89,10 +89,12 @@ fi + # GTest + AC_ARG_WITH(gtest, AS_HELP_STRING([--with-gtest=PATH], + [specify prefix directory for the installed gtest library])) ++gtest_src="/usr/src/gtest" + if test "$with_gtest" -a -d "$with_gtest"; then + gtest_cppflags="-I$with_gtest/include" +- gtest_ldflags="-L$with_gtest/lib" ++ gtest_src="$with_gtest" + fi ++AC_SUBST(GTEST, "$gtest_src") + + AC_ARG_ENABLE(mpich, AS_HELP_STRING([--enable-mpich], + [use MPICH (default is to use Open MPI)])) +@@ -118,7 +120,7 @@ boost_ver=1.55.0 + boost_ver_dir=boost_1_55_0 + AC_SUBST(CPPFLAGS, + "-I$my_abs_srcdir $boost_cppflags $mpi_cppflags $gtest_cppflags $CPPFLAGS -isystem$my_abs_srcdir/$boost_ver_dir") +-AC_SUBST(LDFLAGS, "$mpi_ldflags $gtest_ldflags $LDFLAGS") ++AC_SUBST(LDFLAGS, "$mpi_ldflags $LDFLAGS") + + # Check for the MPI parallel computing library. + libs="$LIBS" +@@ -194,8 +196,7 @@ fi + libs="$LIBS" AC_CHECK_HEADERS([gtest/gtest.h]) AC_CHECK_LIB([pthread], [pthread_create]) - AC_CHECK_LIB([gtest_main],[main]) -+AC_CHECK_LIB([gtest],[main]) - AM_CONDITIONAL([HAVE_GTEST], [test $ac_cv_header_gtest_gtest_h = yes -a $ac_cv_lib_gtest_main_main = yes]) +-AC_CHECK_LIB([gtest_main],[main]) +-AM_CONDITIONAL([HAVE_GTEST], [test $ac_cv_header_gtest_gtest_h = yes -a $ac_cv_lib_gtest_main_main = yes]) ++AM_CONDITIONAL([HAVE_GTEST], [test $ac_cv_header_gtest_gtest_h = yes]) AC_SUBST(GTEST_LIBS, "$LIBS") LIBS=$libs + -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/abyss.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
